<div dir="ltr">Use a dbg build with a debugger and/or valgrind.<div><br></div><div>Dmitry.</div></div><br><div class="gmail_quote"><div dir="ltr">On Mon, Aug 17, 2015 at 11:31 AM Xujun Zhao <<a href="mailto:xzhao99@gmail.com">xzhao99@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">This is run with PETSc opt mode, so the error message looks not very useful, see below:<div>Probably I should use dbg version to see the details.<br><div><br></div><div>
<p><span>[0]PETSC ERROR: ------------------------------------------------------------------------</span></p>
<p><span>[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</span></p>
<p><span>[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</span></p>
<p><span>[0]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a></span></p>
<p><span>[0]PETSC ERROR: or try <a href="http://valgrind.org" target="_blank">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors</span></p>
<p><span>[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run </span></p>
<p><span>[0]PETSC ERROR: to get more information on the crash.</span></p>
<p><span>[1]PETSC ERROR: ------------------------------------------------------------------------</span></p>
<p><span>[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</span></p>
<p><span>[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</span></p>
<p><span>[1]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a></span></p>
<p><span>[1]PETSC ERROR: or try <a href="http://valgrind.org" target="_blank">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors</span></p>
<p><span>[1]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run </span></p>
<p><span>[2]PETSC ERROR: ------------------------------------------------------------------------</span></p>
<p><span>[2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</span></p>
<p><span>[2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</span></p>
<p><span>[2]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a></span></p>
<p><span>[2]PETSC ERROR: or try <a href="http://valgrind.org" target="_blank">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors</span></p>
<p><span>[2]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run </span></p>
<p><span>[2]PETSC ERROR: [1]PETSC ERROR: to get more information on the crash.</span></p>
<p><span>to get more information on the crash.</span></p>
<p><span>[3]PETSC ERROR: ------------------------------------------------------------------------</span></p>
<p><span>[3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</span></p>
<p><span>[3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</span></p>
<p><span>[3]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a></span></p>
<p><span>[3]PETSC ERROR: or try <a href="http://valgrind.org" target="_blank">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors</span></p>
<p><span>[3]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run </span></p>
<p><span>[3]PETSC ERROR: to get more information on the crash.</span></p>
<p><span>[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</span></p>
<p><span>[0]PETSC ERROR: Signal received</span></p>
<p><span>[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</span></p>
<p><span>[0]PETSC ERROR: Petsc Release Version 3.5.4, May, 23, 2015 </span></p>
<p><span>[0]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named <a href="http://mcswl164.mcs.anl.gov" target="_blank">mcswl164.mcs.anl.gov</a> by xzhao Mon Aug 17 11:20:33 2015</span></p>
<p><span>[0]PETSC ERROR: Configure options --with-cc=gcc-4.9 --with-cxx=g++-4.9 --with-fc=gfortran-4.9 --with-cxx-dialect=C++11 --download-mpich --download-fblaslapack --download-scalapack --download-mumps --download-superlu_dist --download-hypre --download-ml --download-parmetis --download-metis --download-triangle --download-chaco --download-elemental --with-debugging=0</span></p>
<p><span>[0]PETSC ERROR: #1 User provided function() line 0 in unknown file</span></p>
<p><span>[1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</span></p>
<p><span>[1]PETSC ERROR: Signal received</span></p>
<p><span>[1]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</span></p>
<p><span>[1]PETSC ERROR: Petsc Release Version 3.5.4, May, 23, 2015 </span></p>
<p><span>[1]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named <a href="http://mcswl164.mcs.anl.gov" target="_blank">mcswl164.mcs.anl.gov</a> by xzhao Mon Aug 17 11:20:33 2015</span></p>
<p><span>[1]PETSC ERROR: Configure options --with-cc=gcc-4.9 --with-cxx=g++-4.9 --with-fc=gfortran-4.9 --with-cxx-dialect=C++11 --download-mpich --download-fblaslapack --download-scalapack --download-mumps --download-superlu_dist --download-hypre --download-ml --download-parmetis --download-metis --download-triangle --download-chaco --download-elemental --with-debugging=0</span></p>
<p><span>[1]PETSC ERROR: #1 User provided function() line 0 in unknown file</span></p>
<p><span>[2]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</span></p>
<p><span>[2]PETSC ERROR: Signal received</span></p>
<p><span>[2]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</span></p>
<p><span>[2]PETSC ERROR: Petsc Release Version 3.5.4, May, 23, 2015 </span></p>
<p><span>[2]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named <a href="http://mcswl164.mcs.anl.gov" target="_blank">mcswl164.mcs.anl.gov</a> by xzhao Mon Aug 17 11:20:33 2015</span></p>
<p><span>[2]PETSC ERROR: Configure options --with-cc=gcc-4.9 --with-cxx=g++-4.9 --with-fc=gfortran-4.9 --with-cxx-dialect=C++11 --download-mpich --download-fblaslapack --download-scalapack --download-mumps --download-superlu_dist --download-hypre --download-ml --download-parmetis --download-metis --download-triangle --download-chaco --download-elemental --with-debugging=0</span></p>
<p><span>[2]PETSC ERROR: #1 User provided function() line 0 in unknown file</span></p>
<p><span>[3]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</span></p>
<p><span>[3]PETSC ERROR: Signal received</span></p>
<p><span>[3]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</span></p>
<p><span>[3]PETSC ERROR: Petsc Release Version 3.5.4, May, 23, 2015 </span></p>
<p><span>[3]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named <a href="http://mcswl164.mcs.anl.gov" target="_blank">mcswl164.mcs.anl.gov</a> by xzhao Mon Aug 17 11:20:33 2015</span></p>
<p><span>[3]PETSC ERROR: Configure options --with-cc=gcc-4.9 --with-cxx=g++-4.9 --with-fc=gfortran-4.9 --with-cxx-dialect=C++11 --download-mpich --download-fblaslapack --download-scalapack --download-mumps --download-superlu_dist --download-hypre --download-ml --download-parmetis --download-metis --download-triangle --download-chaco --download-elemental --with-debugging=0</span></p>
<p><span>[3]PETSC ERROR: #1 User provided function() line 0 in unknown file</span></p>
<p><span>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0</span></p>
<p><span>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1</span></p>
<p><span>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2</span></p>
<p><span>[cli_0]: aborting job:</span></p>
<p><span>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0</span></p>
<p><span>[cli_1]: aborting job:</span></p>
<p><span>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1</span></p>
<p><span>[cli_2]: aborting job:</span></p>
<p><span>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2</span></p>
<p><span>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3</span></p>
<p><span>[cli_3]: aborting job:</span></p>
<p><span>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3</span></p></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Aug 17, 2015 at 11:16 AM, Dmitry Karpeyev <span dir="ltr"><<a href="mailto:dkarpeev@gmail.com" target="_blank">dkarpeev@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Xujun,<div>Regarding your original question: please send the complete error message.</div><span><font color="#888888"><div>Dmitry.</div></font></span></div><div><div><br><div class="gmail_quote"><div dir="ltr">On Mon, Aug 17, 2015 at 11:15 AM Xujun Zhao <<a href="mailto:xzhao99@gmail.com" target="_blank">xzhao99@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Ahhhh, I should drink some coffee in the morning.<div>Now it passed the test!</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Aug 17, 2015 at 11:13 AM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><span>On Mon, Aug 17, 2015 at 11:02 AM, Xujun Zhao <span dir="ltr"><<a href="mailto:xzhao99@gmail.com" target="_blank">xzhao99@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">No. It gives the following error msg:<div></div></div></blockquote><div><br></div></span><div>Did you build the executable?</div><div><br></div><div> cd src/vec/vec/examples/tutorials</div><div> make ex43</div><div><br></div><div> Matt</div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>mpirun -np 2 ex43<br></div><div>
<p><span>[<a href="mailto:proxy%3A0%3A0@mcswl164.mcs.anl.gov" target="_blank">proxy:0:0@mcswl164.mcs.anl.gov</a>] [<a href="mailto:proxy%3A0%3A0@mcswl164.mcs.anl.gov" target="_blank">proxy:0:0@mcswl164.mcs.anl.gov</a>] HYDU_create_process (utils/launch/launch.c:75): HYDU_create_process (utils/launch/launch.c:75): execvp error on file ex43 (No such file or directory)</span></p>
<p><span>execvp error on file ex43 (No such file or directory)</span></p></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Aug 17, 2015 at 10:57 AM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><span>On Mon, Aug 17, 2015 at 10:49 AM, Xujun Zhao <span dir="ltr"><<a href="mailto:xzhao99@gmail.com" target="_blank">xzhao99@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi all,<div><br></div><div>I want PETSc to generate random vector using VecSetRandom() following given examples, but failed and showed some "out of memory" error. The following is the code, which goes well until it reaches VecSetRandom(). Can anyone help me figure out the reason? Thanks a lot.</div></div></blockquote><div><br></div></span><div>Does src/vec/vec/examples/tests/ex43.c run for you?</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><span><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>XZ<br><br><br>--------------------------------------------------------------------------------------------<br> Vec u;<br> PetscRandom rand_ctx; /* random number generator context */<br> PetscMPIInt size, rank;<br> PetscInt n, dn;<br> <br><br> MPI_Comm_rank(PETSC_COMM_WORLD,&rank);//CHKERRQ(ierr);<br> MPI_Comm_size(PETSC_COMM_WORLD,&size);//CHKERRQ(ierr);<br> n = N/size + 1;<br> dn = n*size - N;<br> if ( dn>0 && rank<dn ) n -= 1;<br> printf("--->test in petsc_random_vector(): rank = %d, n = %d\n",rank,n);<br><br><br> VecCreate(PETSC_COMM_WORLD,&u);<br> VecSetSizes(u,n,N);<br> PetscRandomCreate(PETSC_COMM_WORLD, &rand_ctx);<br>#if defined(PETSC_HAVE_DRAND48)<br> PetscRandomSetType(rand_ctx,PETSCRAND48);<br>#elif defined(PETSC_HAVE_RAND)<br> PetscRandomSetType(rand_ctx,PETSCRAND);<br>#endif<br> PetscRandomSetFromOptions(rand_ctx);<br><br><br> VecSetRandom(u,rand_ctx);<br> PetscRandomDestroy(&rand_ctx);<br></div></div>
</blockquote></span></div><span><font color="#888888"><br><br clear="all"><span><font color="#888888"><div><br></div>-- <br><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div>
</font></span></font></span></div></div>
</blockquote></div><br></div>
</blockquote></div></div></div><div><div><br><br clear="all"><div><br></div>-- <br><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div>
</div></div></div></div>
</blockquote></div><br></div>
</blockquote></div>
</div></div></blockquote></div><br></div>
</blockquote></div>